Chromosomal deletions (or "deficiencies") are powerful tools in the genetic analysis of complex genomes. They have been exploited extensively in Drosophila melanogaster, an organism in which deficiencies can be induced and selected efficiently. Spontaneous deletions in humans have facilitated the dissection of phenotypes in contiguous gene syndromes, and led to positional cloning of critical genes. In mice, deletion complexes created by whole animal irradiation experiments have enabled a systematic characterization of functional units along defined chromosomal regions. However, classical mutagenesis in mice is logistically impractical for generating deletion sets on a genome-wide scale. We have developed a high-throughput method for generating radiation-induced deletion complexes at defined regions in the genome using ES cells. Dozens of deletions encompassing a specific locus can be created in a single experiment, ranging in size up to several centiMorgans, and transmitted through the germline. This strategy was implemented to create a set of mice carrying deletions in the proximal t complex region on mouse chromosome 17. In this project, three additional deletion sets along the t complex, each spaced at 5 cM intervals and consisting of 15 different deletions, will be generated. The mice bearing these deletions will be used to genetically localize a series of classical mutations that have hitherto been inaccessible due to recombination suppression associated with t haplotypes. These mutations cause male infertility, hybrid sterility, transmission ratio distortion and severe defects in embryonic development. Additionally, using combinations of overlapping deletions to create homozygous deficiency of small genetic intervals (750 kb, on average), a functional map of the t complex will be generated. These experiments will serve as a paradigm for systematic functional analysis of the mammalian genome, which is the ultimate goal of the genome project.